Contacts of the helix formed by residues 519 - 530 (chain B) in PDB entry 2P1N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 519 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B ASP* 2.6 34.5 + - - -
517B SER 3.6 3.0 + - - -
518B VAL* 1.3 80.3 - - - +
520B PHE* 1.3 63.8 + - - +
521B GLY* 3.4 2.8 + - - -
522B ALA 3.1 15.6 + - - -
523B CYS* 3.3 16.1 + - - -
549B GLU 3.2 13.9 + - - -
550B SER* 4.1 14.8 - - - -
551B CYS 3.5 8.7 - - - -
552B PRO* 4.0 1.3 - - - -
553B VAL* 4.5 0.2 - - - -
496E LYS* 4.1 3.3 + - - +
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Residues in contact with PHE 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B VAL 3.7 0.6 + - - -
519B SER* 1.3 72.1 - - - +
521B GLY* 1.3 64.0 + - - +
523B CYS* 3.1 6.3 + - - +
524B LYS* 3.0 45.3 + - + +
537B VAL* 4.6 4.3 - - + -
544B PRO* 3.7 51.1 - - + +
545B ASP* 4.1 16.8 - - - -
548B PRO 4.9 1.3 - - - +
549B GLU* 3.1 26.0 + - + +
551B CYS 2.9 16.0 + - - +
553B VAL* 3.7 20.6 - - + +
574B TRP* 6.2 0.2 - + - -
576B MET* 3.9 32.3 - - + -
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Residues in contact with GLY 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B SER* 3.1 3.7 - - - -
520B PHE* 1.3 78.4 - - - +
522B ALA* 1.3 55.9 + - - +
524B LYS* 3.2 7.7 + - - +
525B LEU* 3.0 27.7 + - - +
549B GLU* 2.9 43.8 + - - +
496E LYS* 3.9 11.5 - - - -
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Residues in contact with ALA 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B ASP* 3.4 42.6 - - + +
498B LEU* 5.0 3.8 - - + -
499B LEU* 3.8 11.6 - - + +
518B VAL* 4.4 5.6 - - + -
519B SER* 3.1 10.1 + - - +
521B GLY* 1.3 70.9 - - - +
523B CYS* 1.3 61.7 + - - +
525B LEU* 4.4 3.8 - - - -
526B LEU* 2.7 34.2 + - - +
496E LYS* 3.5 13.4 - - + +
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Residues in contact with CYS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B LEU* 5.8 2.0 - - - -
518B VAL* 3.9 13.2 - - - +
519B SER 3.3 14.1 + - - +
520B PHE* 3.1 10.9 + - - +
522B ALA* 1.3 78.4 - - - +
524B LYS* 1.3 62.0 + - - +
526B LEU* 3.5 3.9 + - - +
527B GLY 3.1 17.5 + - - -
535B VAL* 4.1 6.5 - - + +
537B VAL* 3.7 24.7 - - + -
553B VAL* 4.2 8.7 - - - -
556B VAL* 3.2 34.5 - - - -
576B MET* 3.5 17.1 - - + +
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Residues in contact with LYS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B PHE* 3.0 54.8 + - + +
521B GLY* 3.2 5.3 + - - +
523B CYS* 1.3 72.3 - - - +
525B LEU* 1.3 69.6 + - - +
527B GLY* 3.2 3.3 + - - -
528B GLN* 3.2 23.7 + - + +
549B GLU* 3.5 25.1 + - - +
576B MET* 4.1 15.0 - - + +
471E LEU* 6.3 5.6 - - - +
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Residues in contact with LEU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B LEU* 4.4 6.1 - - + -
521B GLY 3.0 16.1 + - - +
522B ALA* 3.8 7.0 - - - +
524B LYS* 1.3 75.3 - - - +
526B LEU* 1.3 64.5 + - - +
528B GLN* 2.9 19.0 + - + +
529B LYS* 2.9 13.8 + - + +
470E ASP* 5.1 4.7 - - + -
471E LEU* 4.5 18.8 - - + +
474E HIS* 3.8 38.4 - - + +
496E LYS* 3.5 40.6 - - + +
497E ALA* 4.0 7.6 - - + +
500E ALA* 3.9 16.2 - - + -
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Residues in contact with LEU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B LEU* 4.0 13.7 - - + +
499B LEU* 3.8 16.7 - - + +
502B ALA* 4.0 18.8 - - + -
505B LEU* 4.0 18.4 - - + -
522B ALA 2.7 22.5 + - - +
523B CYS* 3.9 4.3 - - - +
525B LEU* 1.3 73.4 - - - +
527B GLY* 1.3 60.7 + - - +
528B GLN 3.2 0.2 + - - -
529B LYS* 3.3 4.2 + - + -
530B MET* 2.9 46.6 + - + +
533B LEU* 4.4 0.4 - - + -
535B VAL* 3.9 19.1 - - + -
558B ILE* 3.4 34.3 - - + -
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Residues in contact with GLY 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B CYS 3.1 13.5 + - - -
524B LYS 3.2 1.3 + - - -
525B LEU 3.2 0.6 - - - -
526B LEU* 1.3 75.7 - - - +
528B GLN* 1.3 60.1 + - - +
530B MET 3.6 16.2 + - - +
531B PRO* 3.8 6.4 - - - +
533B LEU 5.2 1.9 - - - +
535B VAL* 4.0 12.7 - - - +
576B MET* 3.5 30.4 - - - +
577B ASP* 4.6 7.0 - - - +
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Residues in contact with GLN 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B LYS* 3.2 13.7 + - + +
525B LEU* 2.9 16.5 + - + +
527B GLY* 1.3 76.0 - - - +
529B LYS* 1.3 67.3 - - - +
530B MET 3.2 1.3 - - - -
531B PRO* 4.0 7.1 - - - +
576B MET 5.6 0.7 - - - +
577B ASP 5.2 4.7 - - - +
578B GLN* 3.9 30.8 + - - +
471E LEU* 4.4 21.9 - - + +
474E HIS* 4.5 13.9 + - - +
475E HIS* 4.4 19.5 - - - -
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Residues in contact with LYS 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B LEU* 5.3 1.8 - - + -
502B ALA* 3.8 24.7 - - + -
503B SER* 5.5 4.7 - - - +
525B LEU* 2.9 11.9 + - + +
526B LEU* 3.8 9.0 - - + +
528B GLN* 1.3 78.7 - - - +
530B MET* 1.3 97.7 + - + +
531B PRO* 2.8 12.4 - - - +
474E HIS* 4.3 21.7 + - + -
478E SER* 6.0 0.8 - - - -
500E ALA* 2.9 39.3 + - + +
501E ASN* 4.1 11.5 - - - +
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Residues in contact with MET 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B ALA* 4.3 15.9 - - + +
503B SER* 4.7 9.6 - - - -
506B GLU* 5.0 15.3 - - - +
526B LEU* 2.9 30.9 + - + +
527B GLY* 3.7 7.1 - - - +
528B GLN 3.2 1.0 - - - -
529B LYS* 1.3 136.7 - - + +
531B PRO* 1.3 59.5 - - + +
532B LYS 3.0 5.6 - - - -
533B LEU* 2.9 57.0 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il